Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 63 of 187
Found at i:18723327 original size:11 final size:10
Alignment explanation
Indices: 18723290--18723348 Score: 73
Period size: 11 Copynumber: 5.5 Consensus size: 10
18723280 ATCTAAATCC
18723290 TTTCTCTCAA
1 TTTCTCTCAA
18723300 TTTCTCTCCAA
1 TTTCTCT-CAA
18723311 TATTCTCTCAAA
1 T-TTCTCTC-AA
18723323 TTTCTCTCAA
1 TTTCTCTCAA
18723333 TTTCCTCTCAA
1 TTT-CTCTCAA
*
18723344 ATTCT
1 TTTCT
18723349 TCTTAAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 14 0.32
11 21 0.48
12 9 0.20
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:18723752 original size:16 final size:16
Alignment explanation
Indices: 18723731--18723763 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
18723721 TGGACCCAAA
18723731 ACTCATCAATGCATTG
1 ACTCATCAATGCATTG
*
18723747 ACTCATCAATGCGTTG
1 ACTCATCAATGCATTG
18723763 A
1 A
18723764 TTGAGAGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (16 bp):
ACTCATCAATGCATTG
Found at i:18724542 original size:7 final size:7
Alignment explanation
Indices: 18724530--18724565 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
18724520 AGATAGTCGA
18724530 TTAGTAT
1 TTAGTAT
18724537 TTAGTAT
1 TTAGTAT
18724544 TTAGTAT
1 TTAGTAT
18724551 TTAGTAT
1 TTAGTAT
18724558 TTAGTAT
1 TTAGTAT
18724565 T
1 T
18724566 ATGTATTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (7 bp):
TTAGTAT
Found at i:18724578 original size:21 final size:20
Alignment explanation
Indices: 18724530--18724572 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 20
18724520 AGATAGTCGA
18724530 TTAGTATTTAGTATTTAGTAT
1 TTAGTATTTAGTA-TTAGTAT
18724551 TTAGTATTTAGTATTATGTAT
1 TTAGTATTTAGTATTA-GTAT
18724572 T
1 T
18724573 ATGTATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (20 bp):
TTAGTATTTAGTATTAGTAT
Found at i:18725226 original size:18 final size:18
Alignment explanation
Indices: 18725189--18725232 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
18725179 ATGCCAGGTG
* *
18725189 TGTATCCTAGCCATTTTA
1 TGTATCCTAACCATTATA
*
18725207 TGTATCCTAACCCTTATA
1 TGTATCCTAACCATTATA
*
18725225 TGTTTCCT
1 TGTATCCT
18725233 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (18 bp):
TGTATCCTAACCATTATA
Found at i:18725519 original size:21 final size:21
Alignment explanation
Indices: 18725473--18725520 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
18725463 CCAACACCGA
*
18725473 CAACCAGATTCCCTACCAGAG
1 CAACCAGAATCCCTACCAGAG
* * *
18725494 GAACCAGAATCCCTGCCGGAG
1 CAACCAGAATCCCTACCAGAG
18725515 CAACCA
1 CAACCA
18725521 CAACCCCCGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.38, G:0.19, T:0.10
Consensus pattern (21 bp):
CAACCAGAATCCCTACCAGAG
Found at i:18729159 original size:126 final size:126
Alignment explanation
Indices: 18728934--18729202 Score: 421
Period size: 126 Copynumber: 2.1 Consensus size: 126
18728924 GGCAAAATAG
*
18728934 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAATACTTTTGCTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAATACTTTTGCTGACAAAGCATC
*
18728999 CTGCTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTACTTGAAATTATTTTTTCAA
66 CTGCTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
* * * * * *
18729060 GAGCTACTGTAGCAAAAGCGCATCCATGTGGGATCTTCTTTTAGTACTTTTGTTGACAATGCATC
1 GAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAATACTTTTGCTGACAAAGCATC
* * *
18729125 CTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCAG
66 CTGCTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
* *
18729186 GAGATACTATAGCAAAA
1 GAGCTACTGTAGCAAAA
18729203 AAAGTCCACG
Statistics
Matches: 130, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 130 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (126 bp):
GAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAATACTTTTGCTGACAAAGCATC
CTGCTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAA
Found at i:18729342 original size:99 final size:98
Alignment explanation
Indices: 18729237--18729555 Score: 382
Period size: 95 Copynumber: 3.3 Consensus size: 98
18729227 AATTAACAAA
* * *
18729237 TAATTTAATTAAGTAACCCTAAACCCTAATTTATTTGAGTTTTCCTTAAAAAAATTTAAACACTG
1 TAATTTAATCAAGTAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAAACTTTAAACACTG
18729302 AACCCTAATCTAATTTTTTTAAAAAATTTATAAT
66 AACCCTAATCTAA-TTTTTTAAAAAATTTATAAT
* * * * *
18729336 TAATTTACTCAAGTAACCCTAGACCCTAATTTATTTGATTTTTCCTTAAAAACCCTT-AACACTA
1 TAATTTAATCAAGTAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAAACTTTAAACACTG
*
18729400 AACCCTAATCTAATTTTTT--AAAATTTTTAAT
66 AACCCTAATCTAATTTTTTAAAAAATTTATAAT
* * * * * *
18729431 TAATTTACTCAAGTAACTCTAAACCCTAATTTAATT-ATTTTTTCTTTAAAAACTATAAACAC-G
1 TAATTTAATCAAGTAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAAACTTTAAACACTG
* *
18729494 AAACCCTACTCTAA-TTTTGAAAAAA-TTATAAT
66 -AACCCTAATCTAATTTTTTAAAAAATTTATAAT
* * * *
18729526 TAATTTAATTAAGAAATCATAAACCCTAAT
1 TAATTTAATCAAGTAACCCTAAACCCTAAT
18729556 CCCTTATTTA
Statistics
Matches: 189, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
94 19 0.10
95 91 0.48
96 4 0.02
97 6 0.03
98 19 0.10
99 50 0.26
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (98 bp):
TAATTTAATCAAGTAACCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAAACTTTAAACACTG
AACCCTAATCTAATTTTTTAAAAAATTTATAAT
Found at i:18729639 original size:27 final size:29
Alignment explanation
Indices: 18729586--18729642 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
18729576 TCTTTAAAAA
*
18729586 CTTAAACCTAAAAACCCCAAAACCCTAAC
1 CTTAAACCTAAAAACCCAAAAACCCTAAC
*
18729615 CTTAAACCT-TAAA-CCAAAAACCCTAAC
1 CTTAAACCTAAAAACCCAAAAACCCTAAC
18729642 C
1 C
18729643 CTAGCAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 14 0.54
28 3 0.12
29 9 0.35
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (29 bp):
CTTAAACCTAAAAACCCAAAAACCCTAAC
Found at i:18731642 original size:100 final size:101
Alignment explanation
Indices: 18731448--18731643 Score: 268
Period size: 100 Copynumber: 2.0 Consensus size: 101
18731438 TTCTTCGACC
* * *
18731448 ATGCCATGGAAATGTCTTCATCAGAGGATGCACTTTATACTTTAATGATGGATTGGGATATTTCA
1 ATGCCATGGAAATGTCTTCATCAGAGGATGCACTTTATACTTCAACGATGGATTGGGACATTTCA
* *
18731513 CGTTCTTACACGCAACACACATGATATTAAACACAT
66 CGTTCTTACACACAACACACATGACATTAAACACAT
* * *
18731549 ATGCCATGGAAATGTTTTCAT-AGAGGATGCACTTTCTACTTCAACGATTGATTGGGACATTTCA
1 ATGCCATGGAAATGTCTTCATCAGAGGATGCACTTTATACTTCAACGATGGATTGGGACATTTCA
* * * * *
18731613 TGTTCTTGCACATAACAGATATGACATTAAA
66 CGTTCTTACACACAACACACATGACATTAAA
18731644 AACTAATATA
Statistics
Matches: 82, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
100 62 0.76
101 20 0.24
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (101 bp):
ATGCCATGGAAATGTCTTCATCAGAGGATGCACTTTATACTTCAACGATGGATTGGGACATTTCA
CGTTCTTACACACAACACACATGACATTAAACACAT
Found at i:18731840 original size:16 final size:18
Alignment explanation
Indices: 18731819--18731858 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
18731809 CTATTACTTA
18731819 TAAATTATAATTT-TA-T
1 TAAATTATAATTTATATT
18731835 TAAA-T-TAATTTATATT
1 TAAATTATAATTTATATT
18731851 TAAATTAT
1 TAAATTAT
18731859 TATGTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 6 0.30
15 3 0.15
16 9 0.45
17 1 0.05
18 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAATTATAATTTATATT
Found at i:18732009 original size:20 final size:17
Alignment explanation
Indices: 18731968--18732002 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
18731958 ATATTTAAGA
*
18731968 TTTTATAAATACTATAT
1 TTTTATAAATAATATAT
18731985 TTTTATAAATAATATAT
1 TTTTATAAATAATATAT
18732002 T
1 T
18732003 ATATTTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTATAAATAATATAT
Found at i:18735278 original size:23 final size:23
Alignment explanation
Indices: 18735245--18735292 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
18735235 TATCTGAAAA
*
18735245 ATTCATATAAATTAATGCATTAAT
1 ATTCATATAAATCAATGCA-TAAT
*
18735269 ATTCA-ATAAATCAATGTATAAT
1 ATTCATATAAATCAATGCATAAT
18735291 AT
1 AT
18735293 AATTAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (23 bp):
ATTCATATAAATCAATGCATAAT
Found at i:18736823 original size:23 final size:23
Alignment explanation
Indices: 18736790--18736837 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
18736780 TATCTGAAAA
*
18736790 ATTCATATAAATTAATGCATTAAT
1 ATTCATATAAATCAATGCA-TAAT
*
18736814 ATTCA-ATAAATCAATGTATAAT
1 ATTCATATAAATCAATGCATAAT
18736836 AT
1 AT
18736838 AATTAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (23 bp):
ATTCATATAAATCAATGCATAAT
Found at i:18737535 original size:19 final size:19
Alignment explanation
Indices: 18737492--18737532 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
18737482 GCTTGAAGAG
* *
18737492 AAATTAATTTTTTTTATAT
1 AAATTAATTTTTTTAAAAT
18737511 AAATTAATTTGTTTTAAAAT
1 AAATTAATTT-TTTTAAAAT
18737531 AA
1 AA
18737533 TTATGGGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
AAATTAATTTTTTTAAAAT
Found at i:18742429 original size:174 final size:174
Alignment explanation
Indices: 18742126--18742802 Score: 872
Period size: 174 Copynumber: 3.9 Consensus size: 174
18742116 CCTCAAGGGT
* * * * *
18742126 CCCCATGGCATATTTTGATTCAGGAAATAGTGATTCCGATGAAGATCTTCCTAAAACAGGTTCAA
1 CCCCATGCCATATTTTGGTCCAGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAA
* * * * * * * * *
18742191 AGGTTCATTCAAGCATTGGTTTTTCTCACAAGACAACTGCCTCCCCGAATTCAGGAAAAGGTTCC
66 AGGCTCATTCAAGCACTAGTTTTTCTCATAAGACAACTGCCTCTCCAAATGCACGAAGAGGTTCC
* * * * * *
18742256 ACTGTTAAAGCTGCAGTTTCCTCCGAATCGACGCTAGTTTCTAA
131 ACTCTTAAAACTACAGTTTCCTCTGAATCGAAGCTAGTTTCTGA
*
18742300 CCCCATACCATATTTTGGTCCAGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAA
1 CCCCATGCCATATTTTGGTCCAGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAA
* * * *
18742365 AGGCTCGTTCAAGCACAATTTTTTCTCATAGGACAACTGCCTCTCCAAATGCACGAAGAGGTTCC
66 AGGCTCATTCAAGCACTAGTTTTTCTCATAAGACAACTGCCTCTCCAAATGCACGAAGAGGTTCC
*
18742430 ACTCTTAAAACTACAGTTTCCTCTGAATCGAAGCTAGTTTTTGA
131 ACTCTTAAAACTACAGTTTCCTCTGAATCGAAGCTAGTTTCTGA
** *
18742474 CCCCATGCCGCATTTTGGTCCAGGAAATAGTGATTCTGATGAAGATCTTCCTAAAATAAGTTCAA
1 CCCCATGCCATATTTTGGTCCAGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAA
* * * * *
18742539 AGGCTCGTTCAAGCA-TGATTTTTTCTCATAGGACAACTGCCTCTCCAAATGCAAGAAGAGTTTC
66 AGGCTCATTCAAGCACT-AGTTTTTCTCATAAGACAACTGCCTCTCCAAATGCACGAAGAGGTTC
* *
18742603 CACTCTTAAAACTACAGTTTCCTCTGAATCAAAGGTAGTTTCTGA
130 CACTCTTAAAACTACAGTTTCCTCTGAATCGAAGCTAGTTTCTGA
* * * * **
18742648 CCCAATGCCATATTTAGGTCCAGGAAACAGTGGTTCTGATGAAGATCTTCCGGAAACAAGTTCAA
1 CCCCATGCCATATTTTGGTCCAGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAA
* * * *
18742713 AGACTCATTCAAGCACTGGTTTTTCTCATAAGACAA-TGGACTCTCCTTCAAATTCACGAAGAGG
66 AGGCTCATTCAAGCACTAGTTTTTCTCATAAGACAACT-G-C-CT-CTCCAAATGCACGAAGAGG
*
18742777 TTCCACTCTTAAAACTACAGTGTCCT
127 TTCCACTCTTAAAACTACAGTTTCCT
18742803 TTGAGCCAGC
Statistics
Matches: 442, Mismatches: 55, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
173 1 0.00
174 397 0.90
175 2 0.00
176 2 0.00
177 40 0.09
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (174 bp):
CCCCATGCCATATTTTGGTCCAGGAAATAGTGATTCTGATGAAGATCTTCCTAAAACAAGTTCAA
AGGCTCATTCAAGCACTAGTTTTTCTCATAAGACAACTGCCTCTCCAAATGCACGAAGAGGTTCC
ACTCTTAAAACTACAGTTTCCTCTGAATCGAAGCTAGTTTCTGA
Found at i:18746417 original size:26 final size:26
Alignment explanation
Indices: 18746388--18746527 Score: 80
Period size: 26 Copynumber: 5.5 Consensus size: 26
18746378 AAGTAGATTA
18746388 TAAATTATATTTAATAATAATTATTT
1 TAAATTATATTTAATAATAATTATTT
* * *
18746414 TAAATTATATTTTATAGT-ATTA-TA
1 TAAATTATATTTAATAATAATTATTT
* * * *
18746438 TAGTATGAT-TTTAGT-A-AATTCA-TA
1 TA-AATTATATTTAATAATAATT-ATTT
* **
18746462 TAAGA--ATATTTAATACTAAGAATTTT
1 TAA-ATTATATTTAATAATAATTA-TTT
18746488 ATCAAATTATATTTAATAATAATTATTT
1 -T-AAATTATATTTAATAATAATTATTT
18746516 TAAATTATATTT
1 TAAATTATATTT
18746528 TATAGTATTA
Statistics
Matches: 84, Mismatches: 17, Indels: 26
0.66 0.13 0.20
Matches are distributed among these distances:
22 2 0.02
23 8 0.10
24 14 0.17
25 10 0.12
26 28 0.33
27 3 0.04
28 5 0.06
29 14 0.17
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (26 bp):
TAAATTATATTTAATAATAATTATTT
Found at i:18746665 original size:145 final size:145
Alignment explanation
Indices: 18746547--18746808 Score: 445
Period size: 145 Copynumber: 1.8 Consensus size: 145
18746537 ATATATTATG
*
18746547 ATTTTAGTAAATTCATATATTTT-ATTAAATTAAATTTAATAATAATTATGTTAAAATATGATTA
1 ATTTTAGTAAATT-ATATATTTTAATTAAAATAAATTTAATAATAATTATGTTAAAATATGATTA
* * *
18746611 AATTATTTATTATTTATATTAATAATCTTATTAAAATTTAATAACAATAATAAATTCATATAATA
65 AATTATTTATTACTGATATTAATAATCTTATTAAAATTTAAAAACAATAATAAATTCATATAATA
18746676 ATATTGATTATTAAGA
130 ATATTGATTATTAAGA
* * *
18746692 ATTTTATTAAATTGTATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAATATGATTAA
1 ATTTTAGTAAATTATATATTTTAATTAAAATAAATTTAATAATAATTATGTTAAAATATGATTAA
18746757 ATTATTTATTACTGATATTAATAATCTTATTAAAATTTAAAAACAATAATAA
66 ATTATTTATTACTGATATTAATAATCTTATTAAAATTTAAAAACAATAATAA
18746809 TAATCATTTA
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
144 8 0.07
145 101 0.93
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (145 bp):
ATTTTAGTAAATTATATATTTTAATTAAAATAAATTTAATAATAATTATGTTAAAATATGATTAA
ATTATTTATTACTGATATTAATAATCTTATTAAAATTTAAAAACAATAATAAATTCATATAATAA
TATTGATTATTAAGA
Found at i:18746980 original size:16 final size:16
Alignment explanation
Indices: 18746959--18747007 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
18746949 TTGATTTGCT
*
18746959 ATTACGCTTCTATTCC
1 ATTACGCATCTATTCC
*
18746975 ATTACGCATCTATTTC
1 ATTACGCATCTATTCC
*
18746991 ATTACGCCTCTATTCC
1 ATTACGCATCTATTCC
18747007 A
1 A
18747008 ATACAGCGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:18747895 original size:22 final size:22
Alignment explanation
Indices: 18747870--18747929 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 22
18747860 TCGAATTAAA
*
18747870 TTTTTATTTAAATTATAATTAT
1 TTTTTATTTAAATTATAAATAT
*
18747892 TTTTATAATATAAA--ATAAATAT
1 TTTT-T-ATTTAAATTATAAATAT
*
18747914 TTTATATATTAAATTA
1 TTTTTAT-TTAAATTA
18747930 GTGAAAATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.07
21 5 0.17
22 14 0.48
23 2 0.07
24 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTTATTTAAATTATAAATAT
Found at i:18748815 original size:26 final size:26
Alignment explanation
Indices: 18748785--18748838 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
18748775 TCGAAATTTT
*
18748785 TTCAAATTGAGTTG-AGTGAAATGAAA
1 TTCAAATTGAGTTGAAATG-AATGAAA
*
18748811 TTCAAGTTGAGTTGAAATGAATGAAA
1 TTCAAATTGAGTTGAAATGAATGAAA
18748837 TT
1 TT
18748839 GTTCGAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (26 bp):
TTCAAATTGAGTTGAAATGAATGAAA
Found at i:18760465 original size:106 final size:106
Alignment explanation
Indices: 18760280--18760491 Score: 406
Period size: 106 Copynumber: 2.0 Consensus size: 106
18760270 TACGATCTAG
18760280 ATGGAAAACAGAACTGCCGAAATCAAGACCACTTATCACATAGAAAATGTGTAAAGCATTCATAA
1 ATGGAAAACAGAACTGCCGAAATCAAGACCACTTATCACATAGAAAATGTGTAAAGCATTCATAA
18760345 ATTCGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCAC
66 ATTCGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCAC
18760386 ATGGAAAACAGAACTGCCGAAATCAAGACCACTTATCACATAGAAAATGTGTAAAGCATTCATAA
1 ATGGAAAACAGAACTGCCGAAATCAAGACCACTTATCACATAGAAAATGTGTAAAGCATTCATAA
* *
18760451 ATTCGGGGCGTTCCGAGAATCGAACTCGGGACCTCTTGCAC
66 ATTCGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCAC
18760492 CCAAAGCGAG
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (106 bp):
ATGGAAAACAGAACTGCCGAAATCAAGACCACTTATCACATAGAAAATGTGTAAAGCATTCATAA
ATTCGGGGCATTCCGAGAATCGAACTCGGGACCTCTCGCAC
Found at i:18768128 original size:22 final size:23
Alignment explanation
Indices: 18768089--18768170 Score: 74
Period size: 20 Copynumber: 3.9 Consensus size: 23
18768079 AATTTAAAAA
18768089 TTTAAAAATATATAAAAATTATT
1 TTTAAAAATATATAAAAATTATT
18768112 TTTAAAAATCAT-T-AAAATTA--
1 TTTAAAAAT-ATATAAAAATTATT
* *
18768132 TTT-AAAA-GTACAAAAA-TATT
1 TTTAAAAATATATAAAAATTATT
18768152 TTT-AAAAT-TATAAAAATTA
1 TTTAAAAATATATAAAAATTA
18768171 ATTAAATGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
17 1 0.02
18 2 0.04
19 8 0.16
20 17 0.35
21 2 0.04
22 7 0.14
23 10 0.20
24 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (23 bp):
TTTAAAAATATATAAAAATTATT
Found at i:18768147 original size:19 final size:19
Alignment explanation
Indices: 18768125--18768176 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
18768115 AAAAATCATT
18768125 AAAATTATTTAAAAGTACA
1 AAAATTATTTAAAAGTACA
* * *
18768144 AAAATATTTTTAAAATTATA
1 AAAAT-TATTTAAAAGTACA
*
18768164 AAAATTAATTAAA
1 AAAATTATTTAAA
18768177 TGTTGACATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATTATTTAAAAGTACA
Found at i:18768170 original size:39 final size:41
Alignment explanation
Indices: 18768066--18768176 Score: 115
Period size: 39 Copynumber: 2.8 Consensus size: 41
18768056 GTCAACATTT
* *
18768066 AATTAATTTTTAAAATT-TAAAAA-T-TTAAAAATATATAAA
1 AATT-ATTTTTAAAATTATAAAAATTATTTAAAATATACAAA
* * *
18768105 AATTATTTTTAAAAATCATTAAAATTATTTAAAA-GTACAAA
1 AATTATTTTT-AAAATTATAAAAATTATTTAAAATATACAAA
*
18768146 AA-TATTTTTAAAATTATAAAAATTAATTAAA
1 AATTATTTTTAAAATTATAAAAATTATTTAAA
18768177 TGTTGACATG
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
38 6 0.10
39 28 0.47
40 12 0.20
41 8 0.13
42 6 0.10
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (41 bp):
AATTATTTTTAAAATTATAAAAATTATTTAAAATATACAAA
Found at i:18768255 original size:20 final size:20
Alignment explanation
Indices: 18768223--18768260 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18768213 GTAATGTCGG
18768223 TAAAAATTAATTAAAAAAAT
1 TAAAAATTAATTAAAAAAAT
18768243 TAAATAATT-ATTAAAAAA
1 TAAA-AATTAATTAAAAAA
18768261 CAAAGAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAAATTAATTAAAAAAAT
Found at i:18771859 original size:17 final size:17
Alignment explanation
Indices: 18771837--18771870 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18771827 TCCTTTCTCA
18771837 TAGGCCTTATGAATAGG
1 TAGGCCTTATGAATAGG
*
18771854 TAGGCCTTATGAGTAGG
1 TAGGCCTTATGAATAGG
18771871 ATAACTGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.29
Consensus pattern (17 bp):
TAGGCCTTATGAATAGG
Found at i:18773219 original size:32 final size:32
Alignment explanation
Indices: 18773156--18773222 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
18773146 CAATCATAAT
* *
18773156 TTTAAAATATATAACAATAGGTTATACTCAAA
1 TTTAAAATATATAACAATAGGTCAAACTCAAA
* *
18773188 TTTAAAATATATAATAATA-GTCAAATTTCAAA
1 TTTAAAATATATAACAATAGGTCAAA-CTCAAA
18773220 TTT
1 TTT
18773223 GATCCTTGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 4 0.13
32 26 0.87
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (32 bp):
TTTAAAATATATAACAATAGGTCAAACTCAAA
Found at i:18773613 original size:15 final size:16
Alignment explanation
Indices: 18773593--18773622 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18773583 TTATTATTTA
18773593 ATTTTTA-TTTAACTT
1 ATTTTTATTTTAACTT
18773608 ATTTTTATTTTAACT
1 ATTTTTATTTTAACT
18773623 ACAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTTATTTTAACTT
Found at i:18777532 original size:23 final size:22
Alignment explanation
Indices: 18777500--18777542 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
18777490 GATAAAACTA
18777500 AACCCCAAAACCCAAAAATAAG
1 AACCCCAAAACCCAAAAATAAG
**
18777522 AACCCTCAAAACGTAAAAATA
1 AACCC-CAAAACCCAAAAATA
18777543 GAATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.58, C:0.28, G:0.05, T:0.09
Consensus pattern (22 bp):
AACCCCAAAACCCAAAAATAAG
Found at i:18777545 original size:22 final size:21
Alignment explanation
Indices: 18777492--18777545 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
18777482 AAGATGGAGA
*
18777492 TAAAACTA-AACCCCAAAACC
1 TAAAAATAGAACCCCAAAACC
* *
18777512 CAAAAATAAGAACCCTCAAAACG
1 TAAAAAT-AGAACCC-CAAAACC
18777535 TAAAAATAGAA
1 TAAAAATAGAA
18777546 TTCTTTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 5 0.19
21 1 0.04
22 9 0.33
23 12 0.44
ACGTcount: A:0.59, C:0.24, G:0.06, T:0.11
Consensus pattern (21 bp):
TAAAAATAGAACCCCAAAACC
Found at i:18782158 original size:9 final size:9
Alignment explanation
Indices: 18782144--18782174 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18782134 GTTAAACGAA
18782144 TCGAGTTAT
1 TCGAGTTAT
*
18782153 TCGAGTTAA
1 TCGAGTTAT
18782162 TCGAGTTAT
1 TCGAGTTAT
18782171 TCGA
1 TCGA
18782175 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:18783585 original size:23 final size:23
Alignment explanation
Indices: 18783504--18783642 Score: 84
Period size: 25 Copynumber: 5.7 Consensus size: 23
18783494 AACCTATAAA
* *
18783504 CATATATATATTATATAATAAAACT
1 CATATATATA-TATAT-ATAACACG
* * * *
18783529 CACACATAATATATATACAAC-CA
1 CATATAT-ATATATATATAACACG
*
18783552 CACATATATATATATATAACACG
1 CATATATATATATATATAACACG
* *
18783575 CATATATATATAT-TACTAACTCCCC
1 CATATATATATATATA-TAA--CACG
* *
18783600 CATTTATATATCATAAATGCAACACG
1 CATATATATAT-ATATAT--AACACG
18783626 CATATATATATATATAT
1 CATATATATATATATAT
18783643 GTATATTGCC
Statistics
Matches: 88, Mismatches: 17, Indels: 18
0.72 0.14 0.15
Matches are distributed among these distances:
22 14 0.16
23 23 0.26
24 3 0.03
25 27 0.31
26 18 0.20
27 1 0.01
28 2 0.02
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (23 bp):
CATATATATATATATATAACACG
Found at i:18783685 original size:61 final size:59
Alignment explanation
Indices: 18783576--18783697 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 59
18783566 TATAACACGC
* * *
18783576 ATATATATATATTACTAACTCCCCCATTTATATATCATAAATGCAACACGCATATATATAT
1 ATATATATATATTACCAACTCCCCCATTTATATATCATAAATACAACACAC-TA-ATATAT
* * * * *
18783637 ATATATGTATATTGCCAACTCCCCCATTTATATATTATATATATAACACACTAATATAT
1 ATATATATATATTACCAACTCCCCCATTTATATATCATAAATACAACACACTAATATAT
18783696 AT
1 AT
18783698 TGTATACAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 8 0.15
60 2 0.04
61 43 0.81
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (59 bp):
ATATATATATATTACCAACTCCCCCATTTATATATCATAAATACAACACACTAATATAT
Found at i:18787346 original size:15 final size:15
Alignment explanation
Indices: 18787316--18787359 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
18787306 ATTATATTAA
*
18787316 AAATATTATTAAATT
1 AAATATTATTTAATT
* *
18787331 ATATATTATTTTATT
1 AAATATTATTTAATT
*
18787346 AAATTTTATTTAAT
1 AAATATTATTTAAT
18787360 AATAATTATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATATTATTTAATT
Found at i:18787425 original size:62 final size:57
Alignment explanation
Indices: 18787300--18787438 Score: 161
Period size: 62 Copynumber: 2.3 Consensus size: 57
18787290 AATTCATATT
* * *
18787300 ATAATAATTATATTAAAAATATTATTAAATTATATATTATTTTATTAAATTTTATTTA
1 ATAATAATTATATT-AAAATATGATTAAATTATATATTATTTTATTAAAATATATTTA
* *
18787358 ATAATAATTATGTTAAAATATGATTAAATTATTTTTTTATTATTTTTATTAAAATATATTTA
1 ATAATAATTATATTAAAATATGATTAAATTA----TATATTA-TTTTATTAAAATATATTTA
* *
18787420 ATAATAATTTTCTTAAAAT
1 ATAATAATTATATTAAAAT
18787439 TTAATAATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
57 16 0.23
58 13 0.19
61 6 0.09
62 34 0.49
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (57 bp):
ATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAAATATATTTA
Found at i:18787599 original size:16 final size:16
Alignment explanation
Indices: 18787575--18787644 Score: 61
Period size: 16 Copynumber: 4.4 Consensus size: 16
18787565 TGAATTACTG
18787575 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
* * *
18787591 ATTATAACTTTATTTC
1 ATTACAACTCTATTCC
*
18787607 ATTACAGCTCTA-TCC
1 ATTACAACTCTATTCC
* * *
18787622 AATTACAGCCCTATTCT
1 -ATTACAACTCTATTCC
18787639 ATTACA
1 ATTACA
18787645 GTGAACCAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
15 2 0.05
16 39 0.91
17 2 0.05
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:18793276 original size:26 final size:26
Alignment explanation
Indices: 18793240--18793292 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
18793230 CCAACGCAAA
18793240 ATAGGATTTAAGCATCCACATAAAGC
1 ATAGGATTTAAGCATCCACATAAAGC
18793266 ATAGGATTTAAGCATCCACATAAAGC
1 ATAGGATTTAAGCATCCACATAAAGC
18793292 A
1 A
18793293 GGTAGAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (26 bp):
ATAGGATTTAAGCATCCACATAAAGC
Found at i:18793369 original size:54 final size:56
Alignment explanation
Indices: 18793286--18793390 Score: 169
Period size: 54 Copynumber: 1.9 Consensus size: 56
18793276 AGCATCCACA
* *
18793286 TAAAGCAGGTAGAAGAAACAATAAGAAAGACTTGCATACCTTTCATGCTCAACATT
1 TAAAGCAGGTACAAGAAACAATAAAAAAGACTTGCATACCTTTCATGCTCAACATT
*
18793342 TAAAGCAGGT-CAA-AAATAATAAAAAAGACTTGCATACCTTTCATGCTCA
1 TAAAGCAGGTACAAGAAACAATAAAAAAGACTTGCATACCTTTCATGCTCA
18793391 GAAGCCAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 34 0.74
55 2 0.04
56 10 0.22
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (56 bp):
TAAAGCAGGTACAAGAAACAATAAAAAAGACTTGCATACCTTTCATGCTCAACATT
Found at i:18813436 original size:44 final size:44
Alignment explanation
Indices: 18813299--18814104 Score: 387
Period size: 44 Copynumber: 18.6 Consensus size: 44
18813289 CCAATGATCC
* ** *
18813299 TATCTCCCTGACGTTGCAGTGGAGTGGATT-A--AATCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGCA-AG-TCT
* * * * *
18813342 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGC-ATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGCAAGTCT
*
18813382 TATCTCCCTGAAGTTGCAGTGGAGCATATTAAGCAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGCAAGTCT
* * * *
18813426 TATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAG-ATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAGCA-AGCAAGTCT
* * * * * *
18813471 TATTTCCCTGAAGTTGAAGTGGAGCAGGTTAAAGC-CG-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAGCAAGCA-AGTCT
* * * * **
18813515 TATCTCCCTGAAGTTGTAATAGAGCAGATTAA--AACCTTGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGC-AAG-TCT
* * * * *
18813559 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGC-ATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGCAAGTCT
*
18813599 TATCTCCCTGAAGTTGCAGTGGAGCATATTAAGCAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGCAAGTCT
* * *
18813643 TATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAG-ATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAGCA-AGCAAGTCT
* * *
18813688 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCGATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGC-A-AGTCT
* * * * * *
18813732 TATCACCCTGAAGTTGCAGTGAAGCAAATTAA--AACCTTAGATAT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGC-AAG-TCT
* * * * * * *
18813776 TATCTCTCTGAAGTTGTAG-AGAGCA-AAT-CG-AATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGCAAGTCT
** * * * *
18813816 TATCTCATTGAAG-TGCAGTAGAGCAGACTAAGTAAGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGCAAGTCT
* * * *
18813859 TATCTCCCTGAAGTTGCAGTGAAGTAGACTGAAG-ATAGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAGCA-AGCAAGTCT
* * * *
18813904 TATCTCCCTGAAGTTGCAGTGAAGTAGACTGAAG-ATAGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAGCA-AGCAAGTCT
* * *
18813949 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACCGATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGC-A-AGTCT
* * * * *
18813993 TATCTTCCTGAAGTTGCAGTGAAGCGGATTAA--AACCTTAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGC-AAG-TCT
* * * * *
18814037 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGC-ATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGCAAGTCT
*
18814077 TATCTCCTTGAAGTTGCAGTGGAGCAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA
18814105 CTAATGGAGT
Statistics
Matches: 604, Mismatches: 111, Indels: 98
0.74 0.14 0.12
Matches are distributed among these distances:
39 4 0.01
40 81 0.13
41 32 0.05
42 25 0.04
43 71 0.12
44 235 0.39
45 150 0.25
46 6 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGCAAGCAAGTCT
Found at i:18813588 original size:217 final size:217
Alignment explanation
Indices: 18813336--18814011 Score: 916
Period size: 217 Copynumber: 3.1 Consensus size: 217
18813326 ATTAAATCAC
18813336 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG
1 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG
*
18813401 TGGAGCATATTAAGCAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCA
66 TGGAGCATATTAAGCAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
* * * * *
18813466 AATCTTATTTCCCTGAAGTTGAAGTGGAGCAGGTTAAAGCCGATAATCCTATCTCCCTGAAGTTG
131 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATAATCCTATCACCCTGAAGTTG
* *
18813531 TAAT-AGAGCAGATTAAAACCTT
196 CAATGA-AGCAAATTAAAACCTT
*
18813553 GGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG
1 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG
18813618 TGGAGCATATTAAGCAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
66 TGGAGCATATTAAGCAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
*
18813683 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCGATAATCCTATCACCCTGAAGTTG
131 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATAATCCTATCACCCTGAAGTTG
*
18813748 CAGTGAAGCAAATTAAAACCTT
196 CAATGAAGCAAATTAAAACCTT
* * * * **
18813770 AGATATTATCTCTCTGAAGTTGTAGAGAGCAAATCGAATCTAGTCTTATCTCATTGAAG-TGCAG
1 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG
* * * * * * * *
18813834 TAGAGCAGACTAAGTAAGCAAATCTTAT-CTCCCTGAAGTTGCAGTGAAGTAGACTGAAGATAGC
66 TGGAGCATATTAAGCAAGCAAGTCTTATCCT-CCTGAAGTTGCAGTGAGGCAGACTGAAGATGGC
* * * * * *
18813898 AAATCTTATCTCCCTGAAGTTGCAGTGAAGTAGACTGAAGATAGC-A-AATCTTATCTCCCTGAA
130 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-A-ACCGATAATCCTATCACCCTGAA
* * * *
18813961 GTTGCAGTGGAGCAGATTAAAACCGAT
192 GTTGCAATGAAGCAAATTAAAACC-TT
*
18813988 A-ATCCTATCT-TCCTGAAGTTGCAG
1 AGATCTTATCTCT-CTGAAGTTGCAG
18814012 TGAAGCGGAT
Statistics
Matches: 414, Mismatches: 38, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
215 2 0.00
216 91 0.22
217 314 0.76
218 5 0.01
219 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (217 bp):
AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG
TGGAGCATATTAAGCAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATAATCCTATCACCCTGAAGTTG
CAATGAAGCAAATTAAAACCTT
Found at i:18813624 original size:84 final size:85
Alignment explanation
Indices: 18813510--18814011 Score: 265
Period size: 89 Copynumber: 5.8 Consensus size: 85
18813500 TAAAGCCGAT
* * * * **
18813510 AATCCTATCTCCCTGAAGTTGTAATAGAGCAGATTAAAACCTTGGATCTTAT-CTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-AAG-TCTTATCCTC-CTGAAGTT
*
18813574 GCAGAGA-GCAGA-TCG-CAT-CT
63 GCAGAGAGGCAGACT-GACATGCA
* * *
18813594 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCATATTAAGCAAGCAAGTCTTATCCTCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AACCAAGTCTTATCCTCCTGAAGTTG
* *
18813659 CAGTGAGGCAGACTGAAGATGGCA
64 CAGAGAGGCAGACTG-ACAT-GCA
* * *
18813683 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCGATAATCCTATCAC-CCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA-CCA-AGTCTTATC-CTCCTGAAGTT
* * * * * * *
18813747 GCAGTGAAGCAAATTAAAACCT-TA
63 GCAGAGAGGCAGACT--GACATGCA
* * * * * * ** * * *
18813771 GATATTATCTCTCTGAAGTTGTAG-AGAGCA-AATCGAATCTAGTCTTAT-CTCATTGAAG-TGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAAGTCTTATCCTC-CTGAAGTTGC
* * *
18813832 AGTAGA-GCAGACTAAGTAAGCA
65 AG-AGAGGCAGACTGA-CATGCA
* * * * *
18813854 AATCTTATCTCCCTGAAGTTGCAGTGAAGTAGACTGAAGATAGCAAATCTTAT-CTCCCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-A-ACCAAGTCTTATCCT-CCTGAAGT
* * * *
18813918 TGCAGTGAAGTAGACTGAAGATAGCA
62 TGCAGAGAGGCAGACTG-ACAT-GCA
* * *
18813944 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATAATCCTATCTTCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC-A-AGTCTTATCCTCCTGAAGTTG
18814009 CAG
64 CAG
18814012 TGAAGCGGAT
Statistics
Matches: 314, Mismatches: 72, Indels: 59
0.71 0.16 0.13
Matches are distributed among these distances:
81 2 0.01
82 1 0.00
83 32 0.10
84 67 0.21
85 11 0.04
86 8 0.03
87 12 0.04
88 42 0.13
89 100 0.32
90 39 0.12
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (85 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCAAGTCTTATCCTCCTGAAGTTGCA
GAGAGGCAGACTGACATGCA
Found at i:18813701 original size:45 final size:45
Alignment explanation
Indices: 18813596--18813969 Score: 275
Period size: 45 Copynumber: 8.5 Consensus size: 45
18813586 TCGCATCTAG
* * *
18813596 TCTTATCTCCCTGAAGTTGCAGTG-GAGCATA-TTAAGCA-AGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGAG-GCAGACTGAAG-ATAGCAAA
*
18813640 TCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGAGGCAGACTGAAGATAGCAAA
* * *
18813685 TCTTATCTCCCTGAAGTTGCAGTG-GAGCAGA-TTAAAATCG-ATAA
1 TCTTATCTCCCTGAAGTTGCAGTGAG-GCAGACTGAAGATAGCA-AA
* * * * * * *
18813729 TCCTATCACCCTGAAGTTGCAGTGAAGCA-AATTAA-A-ACCTTAGA
1 TCTTATCTCCCTGAAGTTGCAGTGAGGCAGACTGAAGATAGC--AAA
* * * * * * *
18813773 TATTATCTCTCTGAAGTTGTAGAGA-GCA-AATCG-A-AT--CTAG
1 TCTTATCTCCCTGAAGTTGCAGTGAGGCAGACT-GAAGATAGCAAA
**
18813813 TCTTATCTCATTGAAG-TGCAGT-AGAGCAGACT-AAG-TAAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGAG-GCAGACTGAAGAT-AGCAAA
* *
18813856 TCTTATCTCCCTGAAGTTGCAGTGAAGTAGACTGAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGAGGCAGACTGAAGATAGCAAA
* *
18813901 TCTTATCTCCCTGAAGTTGCAGTGAAGTAGACTGAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGAGGCAGACTGAAGATAGCAAA
18813946 TCTTATCTCCCTGAAGTTGCAGTG
1 TCTTATCTCCCTGAAGTTGCAGTG
18813970 GAGCAGATTA
Statistics
Matches: 269, Mismatches: 35, Indels: 51
0.76 0.10 0.14
Matches are distributed among these distances:
38 1 0.00
39 4 0.01
40 18 0.07
41 2 0.01
42 1 0.00
43 28 0.10
44 97 0.36
45 116 0.43
46 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGAGGCAGACTGAAGATAGCAAA
Found at i:18813925 original size:261 final size:261
Alignment explanation
Indices: 18813596--18814108 Score: 807
Period size: 261 Copynumber: 2.0 Consensus size: 261
18813586 TCGCATCTAG
* * * *
18813596 TCTTATCTCCCTGAAGTTGCAGTGGAGCATATTAAGCAAGCAAGTCTTATCCTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGATGAAGCAAGCAAATCTTATCCTCCTGAAGTTGCA
* * *
18813661 GTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCGA
66 GTGAAGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGA
18813726 TAATCCTATCACCCTGAAGTTGCAGTGAAGCAAATTAAAACCTTAGATATTATCTCTCTGAAGTT
131 TAATCCTATCACCCTGAAGTTGCAGTGAAGCAAATTAAAACCTTAGATATTATCTCTCTGAAGTT
*
18813791 GTAGAGAGCAAATCGAATCTAGTCTTATCTCATTGAAG-TGCAGTAGAGCAGACTAAGTAAGCAA
196 GCAGAGAGCAAATCGAATCTAGTCTTATCTCATTGAAGTTGCAGTAGAGCAGACTAAGTAAGCAA
18813855 A
261 A
*
18813856 TCTTATCTCCCTGAAGTTGCAGTGAAGTAGACTGAAG-ATAGCAAATCTTAT-CTCCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGA-TGAAGCA-AGCAAATCTTATCCT-CCTGAAGTT
*
18813919 GCAGTGAAGTAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAC
63 GCAGTGAAGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAC
** ** *
18813984 CGATAATCCTATCTTCCTGAAGTTGCAGTGAAGCGGATTAAAACCTTAGATCTTATCTCTCTGAA
128 CGATAATCCTATCACCCTGAAGTTGCAGTGAAGCAAATTAAAACCTTAGATATTATCTCTCTGAA
* * * *
18814049 GTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAA
193 GTTGCAGAGAGCAAATCGAATCTAGTCTTATCTCATTGAAGTTGCAGTAGAGCAGACTAA
18814109 TGGAGTAGTT
Statistics
Matches: 230, Mismatches: 19, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
260 31 0.13
261 182 0.79
262 17 0.07
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (261 bp):
TCTTATCTCCCTGAAGTTGCAGTGAAGCAGATGAAGCAAGCAAATCTTATCCTCCTGAAGTTGCA
GTGAAGCAGACTGAAGATAGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGA
TAATCCTATCACCCTGAAGTTGCAGTGAAGCAAATTAAAACCTTAGATATTATCTCTCTGAAGTT
GCAGAGAGCAAATCGAATCTAGTCTTATCTCATTGAAGTTGCAGTAGAGCAGACTAAGTAAGCAA
A
Found at i:18827385 original size:32 final size:33
Alignment explanation
Indices: 18827349--18827416 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
18827339 CTCTTATACC
*
18827349 ACTGTCTTGGTGACTGTTTCAAATCGTAAA-GG
1 ACTGTCTTGGTGACTGTTTCAAACCGTAAATGG
* *
18827381 ACTGTCTTGGTGATTGTTTTAAACCGTAAATGG
1 ACTGTCTTGGTGACTGTTTCAAACCGTAAATGG
18827414 ACT
1 ACT
18827417 TTTTCAGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 27 0.84
33 5 0.16
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (33 bp):
ACTGTCTTGGTGACTGTTTCAAACCGTAAATGG
Found at i:18827653 original size:114 final size:114
Alignment explanation
Indices: 18827451--18827678 Score: 429
Period size: 114 Copynumber: 2.0 Consensus size: 114
18827441 CTTTATCTGA
18827451 GACTGTAAAACCCTCTGGTTGTTGCATGTAAATATCCTCCTCAAGTTCTCCATGCAAAAATGCAG
1 GACTGTAAAACCCTCTGGTTGTTGCATGTAAATATCCTCCTCAAGTTCTCCATGCAAAAATGCAG
* *
18827516 TTTTTACATCTAACTGCTCAAGCTCCAAATCATGCATGGCCACAATACC
66 TTTTTAAATCTAACTACTCAAGCTCCAAATCATGCATGGCCACAATACC
18827565 GACTGTAAAACCCTCTGGTTGTTGCATGTAAATATCCTCCTCAAGTTCTCCATGCAAAAATGCAG
1 GACTGTAAAACCCTCTGGTTGTTGCATGTAAATATCCTCCTCAAGTTCTCCATGCAAAAATGCAG
*
18827630 TTTTTAAATCTAACTACTTAAGCTCCAAATCATGCATGGCCACAATACC
66 TTTTTAAATCTAACTACTCAAGCTCCAAATCATGCATGGCCACAATACC
18827679 AAGTAAAGCT
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (114 bp):
GACTGTAAAACCCTCTGGTTGTTGCATGTAAATATCCTCCTCAAGTTCTCCATGCAAAAATGCAG
TTTTTAAATCTAACTACTCAAGCTCCAAATCATGCATGGCCACAATACC
Found at i:18836117 original size:13 final size:12
Alignment explanation
Indices: 18836092--18836130 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
18836082 AGCTTCTCTA
18836092 TCTTTCATCTTCT
1 TCTTTC-TCTTCT
18836105 TCTCTTCTCTTCT
1 TCT-TTCTCTTCT
18836118 TCTTTCTCCTTCT
1 TCTTTCT-CTTCT
18836131 CCCTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.17
13 17 0.71
14 3 0.12
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.62
Consensus pattern (12 bp):
TCTTTCTCTTCT
Found at i:18841479 original size:43 final size:44
Alignment explanation
Indices: 18841432--18841535 Score: 106
Period size: 44 Copynumber: 2.4 Consensus size: 44
18841422 TAAAAAAATT
** * * *
18841432 AAAATTTAAAATAATTTAAAAATTC-GAA-AATTTATATTTTTAA
1 AAAATTTAAAATAATAAAAAAATTCAAAAGAAGTTAT-GTTTTAA
*
18841475 AAAATATAAAA-AATAAAAAAATTCTAAAAGAAGTTATGTTTTAA
1 AAAATTTAAAATAATAAAAAAATTC-AAAAGAAGTTATGTTTTAA
18841519 AAAATTTTAAAATAATA
1 AAAA-TTTAAAATAATA
18841536 TGATCTAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
42 11 0.22
43 10 0.20
44 12 0.24
45 12 0.24
46 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.36
Consensus pattern (44 bp):
AAAATTTAAAATAATAAAAAAATTCAAAAGAAGTTATGTTTTAA
Found at i:18843471 original size:21 final size:21
Alignment explanation
Indices: 18843446--18843489 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18843436 GGTTAGATAC
18843446 ATTTAAGATTTAGTA-TTTAAT
1 ATTTAAGATTTAG-AGTTTAAT
*
18843467 ATTTAAGGTTTAGAGTTTAAT
1 ATTTAAGATTTAGAGTTTAAT
18843488 AT
1 AT
18843490 AATTAAGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (21 bp):
ATTTAAGATTTAGAGTTTAAT
Found at i:18843508 original size:23 final size:21
Alignment explanation
Indices: 18843460--18843508 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
18843450 AAGATTTAGT
* *
18843460 ATTTAATATTTAAGGTTTAGA
1 ATTTAATATTTAAGGCTTAAA
*
18843481 GTTTAATATAATTAAGGCTTAAA
1 ATTTAATAT--TTAAGGCTTAAA
18843504 ATTTA
1 ATTTA
18843509 GGGTTTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (21 bp):
ATTTAATATTTAAGGCTTAAA
Found at i:18846523 original size:27 final size:27
Alignment explanation
Indices: 18846492--18846566 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
18846482 TTTCGTAATA
*
18846492 CGCCACAAAGGCTATTCTTTTAGACTT
1 CGCCAAAAAGGCTATTCTTTTAGACTT
* * *
18846519 TGCCAAAAAGGTTATTCTTTTAGGCTT
1 CGCCAAAAAGGCTATTCTTTTAGACTT
** *
18846546 CGCCATGAAGGCTACTCTTTT
1 CGCCAAAAAGGCTATTCTTTT
18846567 CTGACATGTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (27 bp):
CGCCAAAAAGGCTATTCTTTTAGACTT
Found at i:18848882 original size:101 final size:102
Alignment explanation
Indices: 18848767--18848953 Score: 324
Period size: 101 Copynumber: 1.8 Consensus size: 102
18848757 AAAGTGATGG
*
18848767 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACATGTGTAGT
18848830 ACTATGTGCAGGCTACTATGTGTACCGAATAGCTTCGA
65 ACTATGTGCAGGCTACTATGTGTACCGAATAGCTTCGA
* *
18848868 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
18848933 CTATGTGCAGGCTACTATGTG
66 CTATGTGCAGGCTACTATGTG
18848954 AATCGGTATC
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
101 40 0.49
102 37 0.46
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGTGTACCGAATAGCTTCGA
Found at i:18848953 original size:26 final size:26
Alignment explanation
Indices: 18848873--18848953 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
18848863 TTCGATCACG
18848873 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
18848899 CGTGTA-T-CGGATAGTG-ATGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
18848924 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
18848950 TGTG
1 TGTG
18848954 AATCGGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:18848959 original size:51 final size:52
Alignment explanation
Indices: 18848759--18848953 Score: 249
Period size: 51 Copynumber: 3.8 Consensus size: 52
18848749 TGAAAGTGAA
* * *
18848759 AGTGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAT
* *
18848809 A-TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAAT
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAT
* * * * *
18848860 AGCT--TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
1 AG-TGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAT
18848911 AGTGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
18848954 AATCGGTATC
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
49 4 0.03
50 41 0.33
51 77 0.62
52 1 0.01
53 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.31
Consensus pattern (52 bp):
AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAT
Found at i:18849036 original size:46 final size:44
Alignment explanation
Indices: 18848960--18849047 Score: 106
Period size: 46 Copynumber: 2.0 Consensus size: 44
18848950 TGTGAATCGG
*
18848960 TATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCCACCGGA
1 TATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CCACCGGA
* * *
18849004 TATCATTGATTACAAAGTGTGGTTGTTGTGTGCTGAATCCACCG
1 TATCATTAATTA-AAAG-GTGGTTGCTATGTGCTGAATCCACCG
18849048 TGTATCTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 11 0.30
45 3 0.08
46 21 0.57
47 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (44 bp):
TATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCCACCGGA
Found at i:18854172 original size:50 final size:49
Alignment explanation
Indices: 18854065--18854183 Score: 141
Period size: 49 Copynumber: 2.4 Consensus size: 49
18854055 TACCAAAGCT
* * * *
18854065 ATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTACTGCCAATGTC
1 ATGTCCCAGACATGGTCTTACATGCGATGTTTCATATACTGCCAATGTC
* * * *
18854114 ATATCCCAGATATGGTCTTACATGCGA-GTTCTCATATAGGTGCCCATGTC
1 ATGTCCCAGACATGGTCTTACATGCGATGTT-TCATATA-CTGCCAATGTC
18854164 ATGTCCCAGACATGGTCTTA
1 ATGTCCCAGACATGGTCTTA
18854184 TGGGGGACCT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 3 0.05
49 28 0.48
50 27 0.47
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (49 bp):
ATGTCCCAGACATGGTCTTACATGCGATGTTTCATATACTGCCAATGTC
Found at i:18854197 original size:50 final size:50
Alignment explanation
Indices: 18854065--18854351 Score: 254
Period size: 50 Copynumber: 5.6 Consensus size: 50
18854055 TACCAAAGCT
* ** * * * *
18854065 ATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTAC--TGCCAATGTC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCAATGCC
* * * ** * * *
18854114 ATATCCCAGATATGGTCTTACATGCGAGTTCTCATATAGGTGCCCATGTC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGCC
*** * *
18854164 ATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGCC
* * *
18854214 ATATCCCAGACATGGTCTTACATGGGACCTTTCATCTCGGTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGCC
* * * *
18854264 AAGTTCCAGACGTGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTGCCAATGCC
18854320 ATGTCCCAGACATGGTCTTACATGGGACCTCT
1 ATGTCCCAGACATGGTCTTACATGGGACCTCT
18854352 TTACCCAAAT
Statistics
Matches: 190, Mismatches: 40, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
49 28 0.15
50 120 0.63
53 2 0.01
56 40 0.21
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGCC
Found at i:18857363 original size:32 final size:32
Alignment explanation
Indices: 18857322--18857383 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
18857312 CATGTTAATG
18857322 TGTGATGATGCAATATAATTAACAATTTCAAT
1 TGTGATGATGCAATATAATTAACAATTTCAAT
*
18857354 TGTGATGATGCAATATAATTAGCAATTTCA
1 TGTGATGATGCAATATAATTAACAATTTCA
18857384 GTTTAAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (32 bp):
TGTGATGATGCAATATAATTAACAATTTCAAT
Found at i:18857663 original size:91 final size:90
Alignment explanation
Indices: 18857469--18857658 Score: 226
Period size: 91 Copynumber: 2.1 Consensus size: 90
18857459 AGACTCCAGT
* ** ** *
18857469 TTGTGGATAATCCACCAGTG-TTG-ATGGTTAATACGTTGCCGGTAACTGTGAATACACAACGAT
1 TTGTGGATAAACCATGAGTGCTTGCA-GGTTAATACGTTGCCAATAACTGTGAATACACAACAAT
* *
18857532 TTTGCAAATGATAGTTGCCAGTATAAG
65 TTTGCAAATAAAAGTTGCCAG-ATAAG
**
18857559 TTGTGGATAAACCATGAGTGCTTGCAGGTTAATACGTTGCCAATAGTTGTGAATACACAACAATT
1 TTGTGGATAAACCATGAGTGCTTGCAGGTTAATACGTTGCCAATAACTGTGAATACACAACAATT
* *
18857624 TTGCAAATAAAAG-TGCTAG-TAAT
66 TTGCAAATAAAAGTTGCCAGATAAG
18857647 TTGTGGATAAAC
1 TTGTGGATAAAC
18857659 AACCAGTTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
88 15 0.17
90 22 0.26
91 48 0.56
92 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (90 bp):
TTGTGGATAAACCATGAGTGCTTGCAGGTTAATACGTTGCCAATAACTGTGAATACACAACAATT
TTGCAAATAAAAGTTGCCAGATAAG
Found at i:18867904 original size:20 final size:20
Alignment explanation
Indices: 18867852--18867904 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
18867842 CATACATTTG
*
18867852 TTGTTCTGTTCTGCTTTGTT
1 TTGTTCTATTCTGCTTTGTT
* * *
18867872 CTATTCTACTCTGCTTTGTT
1 TTGTTCTATTCTGCTTTGTT
18867892 TTGTTCTATTCTG
1 TTGTTCTATTCTG
18867905 TTGTACTACC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.06, C:0.19, G:0.15, T:0.60
Consensus pattern (20 bp):
TTGTTCTATTCTGCTTTGTT
Found at i:18875314 original size:16 final size:16
Alignment explanation
Indices: 18875293--18875334 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
18875283 AATAATTTGA
*
18875293 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
18875309 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
18875325 TAATTTTAAT
1 TAATTTTAAT
18875335 TTTATTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:18875318 original size:22 final size:23
Alignment explanation
Indices: 18875308--18875363 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
18875298 TTACTAACAA
* *
18875308 TTAATTTTAAT-AACAATTAATT
1 TTAATTTTAATAAAAAAATAATT
*
18875330 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
18875353 TTAATTTTAAT
1 TTAATTTTAAT
18875364 TTTAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:18879885 original size:64 final size:64
Alignment explanation
Indices: 18879759--18879886 Score: 141
Period size: 64 Copynumber: 2.0 Consensus size: 64
18879749 ACGAGCATCC
* * * * * * **
18879759 TGATCGGTATTGATACTGCATGTGTTGCGGGCATACTGCAACTCTTTGTGAGCGTCTTGTTATA
1 TGATCGGTATTAATACTGCATATATTGCAGGCATACTGCAACTCTTTATGAGCATCCCGTTATA
* * *
18879823 TGATCGGTATTAATCCTGCATATATTGCAGGTATACCT-CAACTCTTTATGATCATCCCGTTATA
1 TGATCGGTATTAATACTGCATATATTGCAGGCATA-CTGCAACTCTTTATGAGCATCCCGTTATA
18879887 AGGATCTTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
64 50 0.96
65 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (64 bp):
TGATCGGTATTAATACTGCATATATTGCAGGCATACTGCAACTCTTTATGAGCATCCCGTTATA
Found at i:18880009 original size:24 final size:25
Alignment explanation
Indices: 18879980--18880079 Score: 78
Period size: 25 Copynumber: 4.0 Consensus size: 25
18879970 GAGTTACCTG
*
18879980 TTAAGCTCACATGAGCTTTCTGTT-
1 TTAAGCTCACATGAGCTTCCTGTTA
***
18880004 TTAAGCTTTTATGAGCTTCCTGTTA
1 TTAAGCTCACATGAGCTTCCTGTTA
* ** * *
18880029 TTAAGCCCGGATAAGCTTCCCGTTA
1 TTAAGCTCACATGAGCTTCCTGTTA
* *
18880054 -CATGGCTCACATGAGCTTCCTGTTA
1 TTA-AGCTCACATGAGCTTCCTGTTA
18880079 T
1 T
18880080 ATGGCTCGAG
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
24 21 0.38
25 35 0.62
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (25 bp):
TTAAGCTCACATGAGCTTCCTGTTA
Found at i:18881134 original size:42 final size:42
Alignment explanation
Indices: 18881024--18881120 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
18881014 ACGGGCAGAG
* ** * *
18881024 ACACGGGCATGTCCCTCAGCCGTGTGTCACACACGGCCATGC
1 ACACGGGCGTGTGTCTCAGTCGTGTGTCACACACGACCATGC
* * *
18881066 ACACGGGCGTGTGTCTCAGTCGTGTGTGAGACACGACGATGC
1 ACACGGGCGTGTGTCTCAGTCGTGTGTCACACACGACCATGC
*
18881108 ACACGGGTGTGTG
1 ACACGGGCGTGTG
18881121 GTTTGGTCGT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.20
Consensus pattern (42 bp):
ACACGGGCGTGTGTCTCAGTCGTGTGTCACACACGACCATGC
Found at i:18889580 original size:38 final size:39
Alignment explanation
Indices: 18889533--18889609 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
18889523 TTGTAACAAA
18889533 AATGTTAATGAGTGA-CTAATTTATAACTTTTCGATAAC
1 AATGTTAATGAGTGATCTAATTTATAACTTTTCGATAAC
* * * * *
18889571 AATGTTAATGGGTGATTTGATTTGTCACTTTTCGATAAC
1 AATGTTAATGAGTGATCTAATTTATAACTTTTCGATAAC
18889610 GTTAGTGACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
38 14 0.42
39 19 0.58
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (39 bp):
AATGTTAATGAGTGATCTAATTTATAACTTTTCGATAAC
Found at i:18899980 original size:21 final size:20
Alignment explanation
Indices: 18899956--18900003 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
18899946 AATTTTAAAA
*
18899956 TTTTAACTTTCTTTAT-ATCTT
1 TTTTAAATTT-TTTATAAT-TT
18899977 TTTTAGAATTTTTTATAATTT
1 TTTTA-AATTTTTTATAATTT
18899998 TTTTAA
1 TTTTAA
18900004 TAAAGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 17 0.71
22 6 0.25
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTAAATTTTTTATAATTT
Found at i:18900055 original size:11 final size:12
Alignment explanation
Indices: 18900032--18900067 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
18900022 TTTTAATAAA
18900032 TATTTTGAAATT
1 TATTTTGAAATT
18900044 TATTTT-AAATT
1 TATTTTGAAATT
*
18900055 TATTTTGTAATT
1 TATTTTGAAATT
18900067 T
1 T
18900068 TTATAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (12 bp):
TATTTTGAAATT
Found at i:18901600 original size:13 final size:13
Alignment explanation
Indices: 18901577--18901610 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
18901567 GGATAAGAAC
18901577 AAAGTAAAAAAAAA
1 AAAG-AAAAAAAAA
18901591 AAAGAAAAAAAAA
1 AAAGAAAAAAAAA
*
18901604 AGAGAAA
1 AAAGAAA
18901611 CATATGGCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:18902323 original size:1 final size:1
Alignment explanation
Indices: 18902285--18902314 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
18902275 CAAGGCAAAT
*
18902285 CCCCCCCCCCCCCCCCCCCCCNCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
18902315 GCCGCCCCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:18902809 original size:19 final size:18
Alignment explanation
Indices: 18902785--18902820 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
18902775 CGCTTAATTA
18902785 AAAATGGATGCCTTCTCTC
1 AAAATGGATGCC-TCTCTC
18902804 AAAATGGATGCCTCTCT
1 AAAATGGATGCCTCTCT
18902821 AATCTGCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (18 bp):
AAAATGGATGCCTCTCTC
Found at i:18912335 original size:16 final size:15
Alignment explanation
Indices: 18912300--18912339 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
18912290 ATTTTTAATT
*
18912300 AAATAATTAAAATAA
1 AAATAATTAAAACAA
*
18912315 AAATAGTTAAAACATA
1 AAATAATTAAAACA-A
18912331 AAATAATTA
1 AAATAATTA
18912340 GGAAATGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (15 bp):
AAATAATTAAAACAA
Found at i:18923487 original size:21 final size:22
Alignment explanation
Indices: 18923461--18923507 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
18923451 CTCTGCTCAA
*
18923461 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
18923482 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
18923504 ACTC
1 ACTC
18923508 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:18926696 original size:21 final size:22
Alignment explanation
Indices: 18926670--18926716 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
18926660 CTCTGCTCAA
*
18926670 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
18926691 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
18926713 ACTC
1 ACTC
18926717 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:18929905 original size:21 final size:22
Alignment explanation
Indices: 18929879--18929925 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
18929869 CTCTGCTCAA
*
18929879 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
18929900 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
18929922 ACTC
1 ACTC
18929926 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:18936502 original size:53 final size:52
Alignment explanation
Indices: 18936417--18936546 Score: 163
Period size: 53 Copynumber: 2.4 Consensus size: 52
18936407 AAGTTATTGA
* ** *
18936417 GGTTTGGTGGAAGTAAAAATTTTGGGGAAAAGT-AAAAAGAAAAATATTTTTGG
1 GGTTTGG-GGAAGTAAAAGTTTTGGGGAAAAGTAAAAAAGAAAAA-AAATTGGG
*
18936470 GGTTTGGAGAAGTAAAAGTTTTGGGGAGAAAGTAAAAAAGAAAAAAAATTGGG
1 GGTTTGGGGAAGTAAAAGTTTTGGGGA-AAAGTAAAAAAGAAAAAAAATTGGG
18936523 GGTTTAGGGGGAAGTAAAAGTTTT
1 GGTTT--GGGGAAGTAAAAGTTTT
18936547 TTTGGGGTGA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
52 18 0.27
53 22 0.33
54 11 0.16
55 16 0.24
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.27
Consensus pattern (52 bp):
GGTTTGGGGAAGTAAAAGTTTTGGGGAAAAGTAAAAAAGAAAAAAAATTGGG
Found at i:18937098 original size:12 final size:12
Alignment explanation
Indices: 18937081--18937105 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18937071 GGTGTTCATT
18937081 CGGTTAACCGAC
1 CGGTTAACCGAC
18937093 CGGTTAACCGAC
1 CGGTTAACCGAC
18937105 C
1 C
18937106 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:18937280 original size:9 final size:9
Alignment explanation
Indices: 18937266--18937317 Score: 95
Period size: 9 Copynumber: 5.8 Consensus size: 9
18937256 TTTGGTTAAA
18937266 AATTACCCG
1 AATTACCCG
18937275 AATTACCCG
1 AATTACCCG
18937284 AATTACCCG
1 AATTACCCG
18937293 AATTACCCG
1 AATTACCCG
*
18937302 AATTAACCG
1 AATTACCCG
18937311 AATTACC
1 AATTACC
18937318 GAAAAATACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.37, C:0.31, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:18942370 original size:13 final size:13
Alignment explanation
Indices: 18942352--18942381 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18942342 ACCTCAAATT
*
18942352 TTTGTATTCTTAC
1 TTTGTATTCTAAC
18942365 TTTGTATTCTAAC
1 TTTGTATTCTAAC
18942378 TTTG
1 TTTG
18942382 AATTTAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (13 bp):
TTTGTATTCTAAC
Found at i:18945092 original size:24 final size:24
Alignment explanation
Indices: 18945055--18945116 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
18945045 TGGGAGCCAT
*
18945055 ATATCAGGAAGCTCAAGAGAGCTA
1 ATATCGGGAAGCTCAAGAGAGCTA
* * *
18945079 ATATCGGGATGCTCATGAGAGTTA
1 ATATCGGGAAGCTCAAGAGAGCTA
* *
18945103 TTATCGGGACGCTC
1 ATATCGGGAAGCTC
18945117 TTGCGAGCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (24 bp):
ATATCGGGAAGCTCAAGAGAGCTA
Found at i:18948671 original size:21 final size:21
Alignment explanation
Indices: 18948642--18948684 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18948632 GTTTAATGTC
*
18948642 ACTTCAGTATTTTCATTTTAA
1 ACTTCAGTATTTTCATCTTAA
* *
18948663 ACTTTAGTATTTTTATCTTAA
1 ACTTCAGTATTTTCATCTTAA
18948684 A
1 A
18948685 AAAAATCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (21 bp):
ACTTCAGTATTTTCATCTTAA
Found at i:18949975 original size:16 final size:16
Alignment explanation
Indices: 18949954--18950004 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
18949944 GGTTCACTGG
18949954 AATGGAATAGGGCTGT
1 AATGGAATAGGGCTGT
*
18949970 AATGGAATAGAGCTGT
1 AATGGAATAGGGCTGT
*
18949986 AATGGAATAGGGTTGT
1 AATGGAATAGGGCTGT
18950002 AAT
1 AAT
18950005 AAGTAATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.35, C:0.04, G:0.33, T:0.27
Consensus pattern (16 bp):
AATGGAATAGGGCTGT
Found at i:18956428 original size:71 final size:73
Alignment explanation
Indices: 18956268--18956460 Score: 302
Period size: 71 Copynumber: 2.6 Consensus size: 73
18956258 GAGATTTATT
18956268 TTTTCAGTTGAGGACATAAAACATTCCAATTGACAAGGAAGGACTTTCTTTTCTCTGATTTTGAG
1 TTTTCAGTTGAGGACATAAAACATTCCAATTGACAAGGAAGGACTTTC--TTCTCTGATTTTGAG
18956333 CATAAAAAAG
64 CATAAAAAAG
* * *
18956343 TTTTCAATTGAGGACATAAAACACTCCAATTGACAAGGAAGGAC-TTC-TC-CTTATTTTGAGCA
1 TTTTCAGTTGAGGACATAAAACATTCCAATTGACAAGGAAGGACTTTCTTCTCTGATTTTGAGCA
18956405 TAAAAAAG
66 TAAAAAAG
*
18956413 ATTTTCAGTTGAGGACATAAAACATTCCAATTGACAAGGAAGGGCTTT
1 -TTTTCAGTTGAGGACATAAAACATTCCAATTGACAAGGAAGGACTTT
18956461 TCCAATTTTA
Statistics
Matches: 110, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
70 20 0.18
71 43 0.39
72 2 0.02
74 3 0.03
75 42 0.38
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (73 bp):
TTTTCAGTTGAGGACATAAAACATTCCAATTGACAAGGAAGGACTTTCTTCTCTGATTTTGAGCA
TAAAAAAG
Found at i:18961204 original size:5 final size:5
Alignment explanation
Indices: 18961194--18961237 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
18961184 ACCTAATATG
* *
18961194 TGAAT TGAAT TGAAT TGAAT TGAAT ATGAAT TGTAT TAAAT TGA
1 TGAAT TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGA
18961238 GTTAAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TGAAT
Found at i:18961422 original size:24 final size:24
Alignment explanation
Indices: 18961385--18961435 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
18961375 ATGTTTGAAT
* *
18961385 TAAATTTTAAATATGTG-AATTGTA
1 TAAATGTTAAATATATGAAATTG-A
*
18961409 TAAATGTTATATATATGAAATTGA
1 TAAATGTTAAATATATGAAATTGA
18961433 TAA
1 TAA
18961436 CATATCCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (24 bp):
TAAATGTTAAATATATGAAATTGA
Found at i:18961632 original size:24 final size:25
Alignment explanation
Indices: 18961579--18961626 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
18961569 TTGGCCCTCT
* *
18961579 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATAGCTCTTG
18961604 CGAGCTTCCCGTTA-ATAGCTCTT
1 CGAGCTTCCCGTTATATAGCTCTT
18961627 CGGAGCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.38
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATAGCTCTTG
Found at i:18961719 original size:26 final size:26
Alignment explanation
Indices: 18961684--18961750 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
18961674 ACAGCTCTTA
* *
18961684 TGAGCGTCCCGTTATATGGCTCTTTG
1 TGAGCTTCCCGTTATAAGGCTCTTTG
18961710 TGAGCTTCCCGATTA-AAGGCTCTTTG
1 TGAGCTTCCCG-TTATAAGGCTCTTTG
18961736 TGAGCTTCCCGTTAT
1 TGAGCTTCCCGTTAT
18961751 GGCTCACTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 3 0.08
26 31 0.84
27 3 0.08
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (26 bp):
TGAGCTTCCCGTTATAAGGCTCTTTG
Found at i:18961811 original size:24 final size:23
Alignment explanation
Indices: 18961783--18961863 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 23
18961773 TATAGCTATC
*
18961783 CAGAGCTTCCCATTAATGGCTCTT
1 CAGAGCTTCCCATTAATGGCTC-G
* * * *
18961807 CAGAGCTACCCTTTATTGCCTCG
1 CAGAGCTTCCCATTAATGGCTCG
18961830 CATGAGCTTCCCAATT-ATGGCTCG
1 CA-GAGCTTCCC-ATTAATGGCTCG
18961854 CATGAGCTTC
1 CA-GAGCTTC
18961864 TTGTTATACA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.04
24 42 0.91
25 2 0.04
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.31
Consensus pattern (23 bp):
CAGAGCTTCCCATTAATGGCTCG
Found at i:18964775 original size:41 final size:41
Alignment explanation
Indices: 18964711--18964795 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 41
18964701 AAACATCCTT
* *
18964711 TACCGCTAGGCAGTGTTTCAGTGTCTGCAATGTTGATTTGC
1 TACCACTAGGCAGTGTTTCAGTGTCTACAATGTTGATTTGC
*
18964752 TACCACTAGGCAGTGTTTTAGTGTCTACAATGTTGATTTGC
1 TACCACTAGGCAGTGTTTCAGTGTCTACAATGTTGATTTGC
18964793 TAC
1 TAC
18964796 AATCACTTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
TACCACTAGGCAGTGTTTCAGTGTCTACAATGTTGATTTGC
Found at i:18966688 original size:17 final size:18
Alignment explanation
Indices: 18966662--18966726 Score: 53
Period size: 17 Copynumber: 3.6 Consensus size: 18
18966652 TAACCCATAC
*
18966662 TATTTTTATT-TTTTAAA
1 TATTTATATTATTTTAAA
18966679 TATTTATATTATTTTAATTAA
1 TATTTATATTATTTT-A--AA
* *
18966700 TATTTA-ATAATTTTATA
1 TATTTATATTATTTTAAA
*
18966717 TATTTTTATT
1 TATTTATATT
18966727 GAAATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
17 15 0.39
18 6 0.16
19 2 0.05
20 7 0.18
21 8 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATATTATTTTAAA
Found at i:18979210 original size:21 final size:21
Alignment explanation
Indices: 18979189--18979230 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18979179 TGATGTATTT
*
18979189 AAATAATATTTTATATTTTTTA
1 AAAT-ATATTTTACATTTTTTA
*
18979211 AAATATTTTTTACATTTTTT
1 AAATATATTTTACATTTTTT
18979231 TATTTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
AAATATATTTTACATTTTTTA
Found at i:18979773 original size:35 final size:34
Alignment explanation
Indices: 18979734--18980002 Score: 325
Period size: 35 Copynumber: 8.0 Consensus size: 34
18979724 TTGTCTTTTC
* *
18979734 TTGCAGGGAATATTTCCTGTTCACGCATTATTCTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATT-TG
* * *
18979769 TTGCAGGGAATCTTTCCTGTTCA--CATCATTTC
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
18979801 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTA-TTTG
**
18979836 TTGCAGGGAATCTCTCCTGTTCACATATTATTTTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTA-TTTG
* * *
18979871 TTGCAGGGAATCTTTCCTGTTCA--CATCATTTC
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
*
18979903 TTGCAGGGAATCTCTCCTGTTCACGGATTATTTTG
1 TTGCAGGGAATCTCTCCTGTTCACGCATTA-TTTG
* *
18979938 TTGCAGGGAATCTCTCCTGTTCA--CATCATTTC
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
* *
18979970 TTGCAGGGAATCTCTCCTGTTCATGTATTATTT
1 TTGCAGGGAATCTCTCCTGTTCACGCATTATTT
18980003 CTTTTTGGAC
Statistics
Matches: 205, Mismatches: 21, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
32 74 0.36
33 12 0.06
34 13 0.06
35 106 0.52
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (34 bp):
TTGCAGGGAATCTCTCCTGTTCACGCATTATTTG
Found at i:18979838 original size:67 final size:66
Alignment explanation
Indices: 18979729--18980002 Score: 336
Period size: 67 Copynumber: 4.0 Consensus size: 66
18979719 TTCACTTGTC
* * * * *
18979729 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCAC-
1 TTTTCTTGCAGGGAATCTCTCCTGTTCA--CATCATT-TCTTGCAGGGAATCTCTCCTGTTCACG
*
18979793 ATCA
63 ATTA
* *
18979797 -TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
1 TTTTCTTGCAGGGAATCTCTCCTGTTCA--CATCA-TTTCTTGCAGGGAATCTCTCCTGTTCAC-
*
18979861 TATTA
62 GATTA
* *
18979866 TTTTGTTGCAGGGAATCTTTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCACGGAT
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCAC-GAT
18979931 TA
65 TA
* *
18979933 TTTTGTTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCATGTAT
1 TTTTCTTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCACG-AT
18979998 TA
65 TA
18980000 TTT
1 TTT
18980003 CTTTTTGGAC
Statistics
Matches: 189, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
66 1 0.01
67 154 0.81
68 6 0.03
69 3 0.02
70 25 0.13
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (66 bp):
TTTTCTTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCACGATT
A
Found at i:18979910 original size:102 final size:100
Alignment explanation
Indices: 18979729--18979992 Score: 413
Period size: 102 Copynumber: 2.6 Consensus size: 100
18979719 TTCACTTGTC
* * * *
18979729 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCA--CATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
18979794 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
64 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
18979831 TTTTGTTGCAGGGAATCTCTCCTGTTCACATATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCAC--ATTATTTTGTTGCAGGGAATCTTTCCTGTTCACA
*
18979896 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGGATTA
64 TCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
* * *
18979933 TTTTGTTGCAGGGAATCTCTCCTGTTCACATCA-TTTCTTGCAGGGAATCTCTCCTGTTCA
1 TTTTGTTGCAGGGAATCTCTCCTGTTCACATTATTTTGTTGCAGGGAATCTTTCCTGTTCA
18979993 TGTATTATTT
Statistics
Matches: 152, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
99 25 0.16
100 4 0.03
102 123 0.81
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (100 bp):
TTTTGTTGCAGGGAATCTCTCCTGTTCACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACATC
ATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
Found at i:18982833 original size:21 final size:22
Alignment explanation
Indices: 18982803--18982847 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
18982793 GAGCAAATTG
18982803 TTGATTCTATTTCCTTTTTG-AT
1 TTGATTCTA-TTCCTTTTTGTAT
*
18982825 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCCTTTTTGTAT
18982846 TT
1 TT
18982848 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCCTTTTTGTAT
Found at i:18990618 original size:23 final size:23
Alignment explanation
Indices: 18990586--18990629 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
18990576 ACTACCATTT
*
18990586 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAACAATAATAAATA
* *
18990609 TCTAAGTAAAACATTAATAAA
1 TCTAAATAAAACAATAATAAA
18990630 ATAATATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (23 bp):
TCTAAATAAAACAATAATAAATA
Found at i:18991054 original size:3 final size:3
Alignment explanation
Indices: 18991048--18991085 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
18991038 GATGATGATG
18991048 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
18991086 TTTAATACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:18992403 original size:61 final size:61
Alignment explanation
Indices: 18992332--18992447 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
18992322 ATTTAAAATT
18992332 AAATTAAATTTAATATTTATCTAAATAGTATTTTATCAATTGAATATTAACATGAGATATG
1 AAATTAAATTTAATATTTATCTAAATAGTATTTTATCAATTGAATATTAACATGAGATATG
* * * * * *
18992393 AAATTTAATTTAATATTTATCTAGATATTATTTTATTAATTTAATATTAATATGA
1 AAATTAAATTTAATATTTATCTAAATAGTATTTTATCAATTGAATATTAACATGA
18992448 TTAATTCTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (61 bp):
AAATTAAATTTAATATTTATCTAAATAGTATTTTATCAATTGAATATTAACATGAGATATG
Found at i:18992433 original size:31 final size:31
Alignment explanation
Indices: 18992338--18992440 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
18992328 AATTAAATTA
* * *
18992338 AATTTAATATTTATCTAAATAGTATTTTATC
1 AATTTAATATTTATCTAGATATTATTTTATT
* * * **
18992369 AATTGAATA-TTAACATGAGATATGA-AAT-TT
1 AATTTAATATTTATC-T-AGATATTATTTTATT
18992399 AATTTAATATTTATCTAGATATTATTTTATT
1 AATTTAATATTTATCTAGATATTATTTTATT
18992430 AATTTAATATT
1 AATTTAATATT
18992441 AATATGATTA
Statistics
Matches: 54, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
29 7 0.13
30 15 0.28
31 27 0.50
32 5 0.09
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (31 bp):
AATTTAATATTTATCTAGATATTATTTTATT
Found at i:18993402 original size:24 final size:24
Alignment explanation
Indices: 18993374--18993420 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
18993364 ATATCTTTTT
* *
18993374 ATATTTGTTTTATAATTAT-TTATG
1 ATATTTATATTAT-ATTATATTATG
18993398 ATATTTATATTATATTATATTAT
1 ATATTTATATTATATTATATTAT
18993421 AATTGTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (24 bp):
ATATTTATATTATATTATATTATG
Found at i:18996678 original size:42 final size:42
Alignment explanation
Indices: 18996611--18996712 Score: 95
Period size: 43 Copynumber: 2.4 Consensus size: 42
18996601 AAAAATTTGT
* *
18996611 TAAAAATATAAGAAAAAAATTCAAATATA--TATAAA-TTGAAAA
1 TAAAAATA-AA-AATAAAATTCAAATATAGTTA-AAATTTCAAAA
*
18996653 TAAAAATAAAAATAAAATTAACAAATTTAGTTAAAATTTCAAAA
1 TAAAAATAAAAATAAAATT--CAAATATAGTTAAAATTTCAAAA
*
18996697 -AAAATTAAAAATAAAA
1 TAAAAATAAAAATAAAA
18996713 AAGTTTAATG
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
40 8 0.16
41 2 0.04
42 15 0.29
43 18 0.35
44 8 0.16
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (42 bp):
TAAAAATAAAAATAAAATTCAAATATAGTTAAAATTTCAAAA
Found at i:18996734 original size:37 final size:36
Alignment explanation
Indices: 18996649--18996735 Score: 84
Period size: 37 Copynumber: 2.3 Consensus size: 36
18996639 ATATAAATTG
* * * *
18996649 AAAATAAAAATAAAAATAAAATTAACAAATTTAGTTA
1 AAAATAAAAA-AAAAATAAAAATAAAAAATTTAATGA
* * *
18996686 AAATTTCAAAAAAAATTAAAAATAAAAAAGTTTAATGA
1 AAA-ATAAAAAAAAAATAAAAATAAAAAA-TTTAATGA
18996724 AAAATAAAAAAA
1 AAAATAAAAAAA
18996736 TAAAATTGGT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
37 25 0.64
38 14 0.36
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.24
Consensus pattern (36 bp):
AAAATAAAAAAAAAATAAAAATAAAAAATTTAATGA
Found at i:18996962 original size:2 final size:2
Alignment explanation
Indices: 18996957--18996981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18996947 ATTACTTATT
18996957 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18996982 TAGTTTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19000324 original size:14 final size:14
Alignment explanation
Indices: 19000292--19000325 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
19000282 ATATTTTCAA
19000292 AATATTAAAATATG
1 AATATTAAAATATG
19000306 AATATATAAAATATG
1 AATAT-TAAAATATG
19000321 -ATATT
1 AATATT
19000326 TTACTAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 9 0.47
15 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (14 bp):
AATATTAAAATATG
Found at i:19008482 original size:20 final size:20
Alignment explanation
Indices: 19008445--19008487 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
19008435 TTTCTTTTTA
* *
19008445 ATTGTTAATATTTTTTAATT
1 ATTGTTAATATTTGTTAAAT
19008465 ATTGTTAA-ATTTAGTTAAAT
1 ATTGTTAATATTT-GTTAAAT
19008485 ATT
1 ATT
19008488 TTGAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (20 bp):
ATTGTTAATATTTGTTAAAT
Found at i:19020351 original size:18 final size:17
Alignment explanation
Indices: 19020328--19020369 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
19020318 GGTTTATTGA
* *
19020328 TTTATTTCTTTGTTTATT
1 TTTATTTATTTATTTA-T
19020346 TTTATTTATTTATTTAT
1 TTTATTTATTTATTTAT
19020363 TTTATTT
1 TTTATTT
19020370 TTATTCCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTATTTATTTATTTAT
Found at i:19020353 original size:4 final size:4
Alignment explanation
Indices: 19020320--19020369 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
19020310 TCCTGATTGG
* * *
19020320 TTTA TTGA TTTA TTTC TTTG TTTA -TT- TTTA TTTA TTTA TTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA
19020367 TTT
1 TTT
19020370 TTATTCCATC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
3 4 0.11
4 30 0.79
5 4 0.11
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:19020355 original size:22 final size:23
Alignment explanation
Indices: 19020327--19020374 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
19020317 TGGTTTATTG
*
19020327 ATTTATTTCTTT-GTTTATTTTT
1 ATTTATTTATTTAGTTTATTTTT
*
19020349 ATTTATTTATTTATTTTATTTTT
1 ATTTATTTATTTAGTTTATTTTT
19020372 ATT
1 ATT
19020375 CCATCAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (23 bp):
ATTTATTTATTTAGTTTATTTTT
Found at i:19022367 original size:26 final size:26
Alignment explanation
Indices: 19022310--19022368 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
19022300 ATATTATTGA
*
19022310 TATATGATATGTGATATGAATTATGT
1 TATATGATATGTGATATCAATTATGT
* *
19022336 TATATGATATTTGATATCTATATATGT
1 TATATGATATGTGATATCAAT-TATGT
19022363 T-TATGA
1 TATATGA
19022369 ATTGATGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (26 bp):
TATATGATATGTGATATCAATTATGT
Found at i:19025399 original size:43 final size:43
Alignment explanation
Indices: 19025333--19025492 Score: 143
Period size: 43 Copynumber: 3.7 Consensus size: 43
19025323 AGCTCTTACA
* *
19025333 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACTGTCCCAGACAG-GGTCTTACACGAAATCAAATA-CG
**
19025376 ATGCC-ACTGTCCCAGACAGGGTCTTACACGAAATCGTATACG
1 ATGCCAACTGTCCCAGACAGGGTCTTACACGAAATCAAATACG
* * *
19025418 ATGCCGA-TGTCCCAGACATGGTCTTATACGTAAATCTCAAAT-CG
1 ATGCCAACTGTCCCAGACAGGGTCTTACACG-AAA--TCAAATACG
* * *
19025462 ACGCCAAC-GTCCCAGATATGGTCTTACACGA
1 ATGCCAACTGTCCCAGACAGGGTCTTACACGA
19025493 TAACTCATAT
Statistics
Matches: 98, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
42 30 0.31
43 36 0.37
44 28 0.29
45 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCCAACTGTCCCAGACAGGGTCTTACACGAAATCAAATACG
Found at i:19028141 original size:9 final size:9
Alignment explanation
Indices: 19028127--19028183 Score: 71
Period size: 9 Copynumber: 6.2 Consensus size: 9
19028117 TTTGGTTAAA
19028127 AATTACCCG
1 AATTACCCG
19028136 AATTACCCG
1 AATTACCCG
*
19028145 AATTAACCG
1 AATTACCCG
19028154 AATTA-CCG
1 AATTACCCG
*
19028162 AAAAATACCCG
1 --AATTACCCG
19028173 AATTACCCG
1 AATTACCCG
19028182 AA
1 AA
19028184 ATTTTTTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 3 0.07
9 32 0.76
10 4 0.10
11 3 0.07
ACGTcount: A:0.42, C:0.28, G:0.11, T:0.19
Consensus pattern (9 bp):
AATTACCCG
Found at i:19028345 original size:13 final size:13
Alignment explanation
Indices: 19028327--19028356 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
19028317 TTTTAGTTTT
19028327 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
19028340 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
19028353 ATTG
1 ATTG
19028357 AGTTCCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:19041377 original size:22 final size:22
Alignment explanation
Indices: 19041349--19041402 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
19041339 TATGCATGTA
19041349 AGTGATTTTAGCTTCTGTTTTT
1 AGTGATTTTAGCTTCTGTTTTT
19041371 AGTGATTTTAGCTTCTGTTTTT
1 AGTGATTTTAGCTTCTGTTTTT
*
19041393 AGTAATTTTA
1 AGTGATTTTA
19041403 TGTTTTTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.07, G:0.17, T:0.57
Consensus pattern (22 bp):
AGTGATTTTAGCTTCTGTTTTT
Found at i:19055201 original size:20 final size:20
Alignment explanation
Indices: 19055178--19055219 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19055168 AAAAATAGGG
* *
19055178 CTTTTTTTTGTAATTTGTCC
1 CTTTTTTTGGTAATTTGCCC
*
19055198 CTTTTTTTGGTATTTTGCCC
1 CTTTTTTTGGTAATTTGCCC
19055218 CT
1 CT
19055220 AATAATACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.19, G:0.12, T:0.62
Consensus pattern (20 bp):
CTTTTTTTGGTAATTTGCCC
Found at i:19055263 original size:19 final size:20
Alignment explanation
Indices: 19055241--19055302 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 20
19055231 TTAATGTATT
19055241 ATTATAATA-TGTAGCTCAA
1 ATTATAATATTGTAGCTCAA
* *
19055260 ATTAT-GTATTGTAG-TTAA
1 ATTATAATATTGTAGCTCAA
19055278 TATTCATAATATTGTAGCTCAA
1 -ATT-ATAATATTGTAGCTCAA
19055300 ATT
1 ATT
19055303 GTCAATCCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 5 0.15
19 13 0.38
20 2 0.06
21 11 0.32
22 3 0.09
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (20 bp):
ATTATAATATTGTAGCTCAA
Found at i:19056670 original size:22 final size:22
Alignment explanation
Indices: 19056642--19056733 Score: 89
Period size: 22 Copynumber: 4.1 Consensus size: 22
19056632 GAATATTCAA
19056642 AAAATAATAATAAAATAGTAGC
1 AAAATAATAATAAAATAGTAGC
* *
19056664 AATATAATAGTAAAAT-GATAGC
1 AAAATAATAATAAAATAG-TAGC
* *
19056686 AAAACAATGAA-AAGAATAGTGGC
1 AAAATAAT-AATAA-AATAGTAGC
* *
19056709 AAAATAATAAAAAAATAGCAGC
1 AAAATAATAATAAAATAGTAGC
19056731 AAA
1 AAA
19056734 TCTTTTTGCA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
21 1 0.02
22 38 0.68
23 16 0.29
24 1 0.02
ACGTcount: A:0.62, C:0.07, G:0.13, T:0.18
Consensus pattern (22 bp):
AAAATAATAATAAAATAGTAGC
Found at i:19067948 original size:19 final size:19
Alignment explanation
Indices: 19067906--19067949 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
19067896 AATTTTGAAT
*
19067906 AAAAATAGATAAAATTTTG
1 AAAAATAGATAAAATTGTG
*
19067925 AAAAATAGATAACA-TGTG
1 AAAAATAGATAAAATTGTG
19067943 AGAAAAT
1 A-AAAAT
19067950 GAGGGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (19 bp):
AAAAATAGATAAAATTGTG
Found at i:19068933 original size:21 final size:22
Alignment explanation
Indices: 19068893--19068934 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
19068883 CTGATTTTTA
*
19068893 CTAATTTATTGCATATAAACTG
1 CTAATTTATTGCATACAAACTG
*
19068915 CTAATTT-TTGCGTACAAACT
1 CTAATTTATTGCATACAAACT
19068935 TGTTGGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (22 bp):
CTAATTTATTGCATACAAACTG
Found at i:19071138 original size:125 final size:124
Alignment explanation
Indices: 19070916--19071171 Score: 345
Period size: 125 Copynumber: 2.1 Consensus size: 124
19070906 AAATAGTGGG
** * * * *
19070916 AAATCGCTTCTACTAGGATGCTATTTAAGAAGAAATTGTGAAATAGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
*
19070981 TCGCTACAGTGGTAATGTGAGAAATAATTTTTTTTTGACGTTTTATGAGGAAATAGTATA
66 TCGCTACAGTGGTAATGTGAGAAATAATTTTTTTTTGACG-TTTATGAGCAAATAGTATA
* * *
19071041 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACTCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
* * * *
19071106 TCGCTACAGTTGGTCATGTTG-GAAATAA-TTTTTTTTGACGTTTCTGAGCAAATAGTGTC
66 TCGCTACAG-TGGTAATG-TGAGAAATAATTTTTTTTTGACGTTTATGAGCAAATAGTATA
19071165 AAATCGC
1 AAATCGC
19071172 GCCCTCGTGG
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
124 22 0.19
125 77 0.67
126 14 0.12
127 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (124 bp):
AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
TCGCTACAGTGGTAATGTGAGAAATAATTTTTTTTTGACGTTTATGAGCAAATAGTATA
Found at i:19076387 original size:21 final size:21
Alignment explanation
Indices: 19076363--19076403 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19076353 ATATGTAGCG
19076363 TGATACGATATGTATGATCTA
1 TGATACGATATGTATGATCTA
* *
19076384 TGATACGATTTGTCTGATCT
1 TGATACGATATGTATGATCT
19076404 GTTACTTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (21 bp):
TGATACGATATGTATGATCTA
Done.